One thing that is still not known about the Robert E. Lee family is the Y-DNA of his maternal Carter line.
I think it is fairly well accepted that the Carter line for General Lee goes like this:
1 - Robert "King" Carter & Judith Armistead
2 - John "Secretary" Carter of Corotoman Plantation & Elizabeth Hill
3 - Charles Carter of Shirley Plantation & Anne Butler Moore
4 - Anne Hill Carter & Henry Lee, III
5 - Robert E. Lee
There is a new group on Yahoo with the goal of identifying the Y-DNA of Robert "King" Carter of Virginia.http://groups.yahoo.com/group/RKCVA/
Anyone with an interest in this topic is welcome to join.